3JAR
Cryo-EM structure of GDP-microtubule co-polymerized with EB3
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0000226 | biological_process | microtubule cytoskeleton organization |
| A | 0000278 | biological_process | mitotic cell cycle |
| A | 0003924 | molecular_function | GTPase activity |
| A | 0005200 | molecular_function | structural constituent of cytoskeleton |
| A | 0005525 | molecular_function | GTP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005856 | cellular_component | cytoskeleton |
| A | 0005874 | cellular_component | microtubule |
| A | 0007017 | biological_process | microtubule-based process |
| A | 0015630 | cellular_component | microtubule cytoskeleton |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0000226 | biological_process | microtubule cytoskeleton organization |
| B | 0000278 | biological_process | mitotic cell cycle |
| B | 0003924 | molecular_function | GTPase activity |
| B | 0005200 | molecular_function | structural constituent of cytoskeleton |
| B | 0005515 | molecular_function | protein binding |
| B | 0005525 | molecular_function | GTP binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005856 | cellular_component | cytoskeleton |
| B | 0005874 | cellular_component | microtubule |
| B | 0007017 | biological_process | microtubule-based process |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0000226 | biological_process | microtubule cytoskeleton organization |
| C | 0000278 | biological_process | mitotic cell cycle |
| C | 0003924 | molecular_function | GTPase activity |
| C | 0005200 | molecular_function | structural constituent of cytoskeleton |
| C | 0005525 | molecular_function | GTP binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005856 | cellular_component | cytoskeleton |
| C | 0005874 | cellular_component | microtubule |
| C | 0007017 | biological_process | microtubule-based process |
| C | 0015630 | cellular_component | microtubule cytoskeleton |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0000226 | biological_process | microtubule cytoskeleton organization |
| D | 0000278 | biological_process | mitotic cell cycle |
| D | 0003924 | molecular_function | GTPase activity |
| D | 0005200 | molecular_function | structural constituent of cytoskeleton |
| D | 0005515 | molecular_function | protein binding |
| D | 0005525 | molecular_function | GTP binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005856 | cellular_component | cytoskeleton |
| D | 0005874 | cellular_component | microtubule |
| D | 0007017 | biological_process | microtubule-based process |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0000166 | molecular_function | nucleotide binding |
| E | 0000226 | biological_process | microtubule cytoskeleton organization |
| E | 0000278 | biological_process | mitotic cell cycle |
| E | 0003924 | molecular_function | GTPase activity |
| E | 0005200 | molecular_function | structural constituent of cytoskeleton |
| E | 0005525 | molecular_function | GTP binding |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0005856 | cellular_component | cytoskeleton |
| E | 0005874 | cellular_component | microtubule |
| E | 0007017 | biological_process | microtubule-based process |
| E | 0015630 | cellular_component | microtubule cytoskeleton |
| E | 0016787 | molecular_function | hydrolase activity |
| E | 0046872 | molecular_function | metal ion binding |
| F | 0000166 | molecular_function | nucleotide binding |
| F | 0000226 | biological_process | microtubule cytoskeleton organization |
| F | 0000278 | biological_process | mitotic cell cycle |
| F | 0003924 | molecular_function | GTPase activity |
| F | 0005200 | molecular_function | structural constituent of cytoskeleton |
| F | 0005515 | molecular_function | protein binding |
| F | 0005525 | molecular_function | GTP binding |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0005856 | cellular_component | cytoskeleton |
| F | 0005874 | cellular_component | microtubule |
| F | 0007017 | biological_process | microtubule-based process |
| F | 0046872 | molecular_function | metal ion binding |
| G | 0000166 | molecular_function | nucleotide binding |
| G | 0000226 | biological_process | microtubule cytoskeleton organization |
| G | 0000278 | biological_process | mitotic cell cycle |
| G | 0003924 | molecular_function | GTPase activity |
| G | 0005200 | molecular_function | structural constituent of cytoskeleton |
| G | 0005515 | molecular_function | protein binding |
| G | 0005525 | molecular_function | GTP binding |
| G | 0005737 | cellular_component | cytoplasm |
| G | 0005856 | cellular_component | cytoskeleton |
| G | 0005874 | cellular_component | microtubule |
| G | 0007017 | biological_process | microtubule-based process |
| G | 0046872 | molecular_function | metal ion binding |
| H | 0000166 | molecular_function | nucleotide binding |
| H | 0000226 | biological_process | microtubule cytoskeleton organization |
| H | 0000278 | biological_process | mitotic cell cycle |
| H | 0003924 | molecular_function | GTPase activity |
| H | 0005200 | molecular_function | structural constituent of cytoskeleton |
| H | 0005515 | molecular_function | protein binding |
| H | 0005525 | molecular_function | GTP binding |
| H | 0005737 | cellular_component | cytoplasm |
| H | 0005856 | cellular_component | cytoskeleton |
| H | 0005874 | cellular_component | microtubule |
| H | 0007017 | biological_process | microtubule-based process |
| H | 0046872 | molecular_function | metal ion binding |
| I | 0000166 | molecular_function | nucleotide binding |
| I | 0000226 | biological_process | microtubule cytoskeleton organization |
| I | 0000278 | biological_process | mitotic cell cycle |
| I | 0003924 | molecular_function | GTPase activity |
| I | 0005200 | molecular_function | structural constituent of cytoskeleton |
| I | 0005515 | molecular_function | protein binding |
| I | 0005525 | molecular_function | GTP binding |
| I | 0005737 | cellular_component | cytoplasm |
| I | 0005856 | cellular_component | cytoskeleton |
| I | 0005874 | cellular_component | microtubule |
| I | 0007017 | biological_process | microtubule-based process |
| I | 0046872 | molecular_function | metal ion binding |
| J | 0000166 | molecular_function | nucleotide binding |
| J | 0000226 | biological_process | microtubule cytoskeleton organization |
| J | 0000278 | biological_process | mitotic cell cycle |
| J | 0003924 | molecular_function | GTPase activity |
| J | 0005200 | molecular_function | structural constituent of cytoskeleton |
| J | 0005525 | molecular_function | GTP binding |
| J | 0005737 | cellular_component | cytoplasm |
| J | 0005856 | cellular_component | cytoskeleton |
| J | 0005874 | cellular_component | microtubule |
| J | 0007017 | biological_process | microtubule-based process |
| J | 0015630 | cellular_component | microtubule cytoskeleton |
| J | 0016787 | molecular_function | hydrolase activity |
| J | 0046872 | molecular_function | metal ion binding |
| K | 0000166 | molecular_function | nucleotide binding |
| K | 0000226 | biological_process | microtubule cytoskeleton organization |
| K | 0000278 | biological_process | mitotic cell cycle |
| K | 0003924 | molecular_function | GTPase activity |
| K | 0005200 | molecular_function | structural constituent of cytoskeleton |
| K | 0005525 | molecular_function | GTP binding |
| K | 0005737 | cellular_component | cytoplasm |
| K | 0005856 | cellular_component | cytoskeleton |
| K | 0005874 | cellular_component | microtubule |
| K | 0007017 | biological_process | microtubule-based process |
| K | 0015630 | cellular_component | microtubule cytoskeleton |
| K | 0016787 | molecular_function | hydrolase activity |
| K | 0046872 | molecular_function | metal ion binding |
| L | 0000166 | molecular_function | nucleotide binding |
| L | 0000226 | biological_process | microtubule cytoskeleton organization |
| L | 0000278 | biological_process | mitotic cell cycle |
| L | 0003924 | molecular_function | GTPase activity |
| L | 0005200 | molecular_function | structural constituent of cytoskeleton |
| L | 0005525 | molecular_function | GTP binding |
| L | 0005737 | cellular_component | cytoplasm |
| L | 0005856 | cellular_component | cytoskeleton |
| L | 0005874 | cellular_component | microtubule |
| L | 0007017 | biological_process | microtubule-based process |
| L | 0015630 | cellular_component | microtubule cytoskeleton |
| L | 0016787 | molecular_function | hydrolase activity |
| L | 0046872 | molecular_function | metal ion binding |
| M | 0008017 | molecular_function | microtubule binding |
| N | 0008017 | molecular_function | microtubule binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE GTP E 501 |
| Chain | Residue |
| E | GLY10 |
| E | GLY143 |
| E | GLY144 |
| E | THR145 |
| E | GLY146 |
| E | ILE171 |
| E | THR179 |
| E | GLU183 |
| E | ASN206 |
| E | TYR224 |
| E | ASN228 |
| E | GLN11 |
| E | MG502 |
| G | LEU248 |
| G | LYS254 |
| E | ALA12 |
| E | GLN15 |
| E | ASP98 |
| E | ALA99 |
| E | ALA100 |
| E | ASN101 |
| E | SER140 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG E 502 |
| Chain | Residue |
| E | GLU71 |
| E | GTP501 |
| site_id | AC3 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE GDP F 501 |
| Chain | Residue |
| F | GLN11 |
| F | CYS12 |
| F | GLN15 |
| F | SER140 |
| F | GLY143 |
| F | GLY144 |
| F | THR145 |
| F | GLY146 |
| F | ASP179 |
| F | ASN206 |
| F | TYR224 |
| F | ASN228 |
| site_id | AC4 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE GTP J 501 |
| Chain | Residue |
| F | LEU248 |
| F | LYS254 |
| J | GLN11 |
| J | ALA12 |
| J | GLN15 |
| J | ALA99 |
| J | ASN101 |
| J | SER140 |
| J | GLY143 |
| J | GLY144 |
| J | THR145 |
| J | GLY146 |
| J | ILE171 |
| J | THR179 |
| J | GLU183 |
| J | ASN206 |
| J | TYR224 |
| J | ASN228 |
| J | MG502 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG J 502 |
| Chain | Residue |
| J | GLU71 |
| J | GTP501 |
| site_id | AC6 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE GDP G 501 |
| Chain | Residue |
| G | GLN11 |
| G | CYS12 |
| G | GLN15 |
| G | SER140 |
| G | GLY143 |
| G | GLY144 |
| G | THR145 |
| G | GLY146 |
| G | ASP179 |
| G | ASN206 |
| G | TYR224 |
| G | ASN228 |
| site_id | AC7 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE GTP C 501 |
| Chain | Residue |
| C | GLN11 |
| C | ALA12 |
| C | GLN15 |
| C | ALA99 |
| C | ALA100 |
| C | ASN101 |
| C | SER140 |
| C | GLY143 |
| C | GLY144 |
| C | THR145 |
| C | GLY146 |
| C | ILE171 |
| C | THR179 |
| C | GLU183 |
| C | ASN206 |
| C | TYR224 |
| C | ASN228 |
| C | MG502 |
| I | LEU248 |
| I | LYS254 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG C 502 |
| Chain | Residue |
| C | GLU71 |
| C | GTP501 |
| site_id | AC9 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE GDP D 501 |
| Chain | Residue |
| D | ASP179 |
| D | ASN206 |
| D | TYR224 |
| D | ASN228 |
| D | GLN11 |
| D | CYS12 |
| D | GLN15 |
| D | SER140 |
| D | GLY143 |
| D | GLY144 |
| D | THR145 |
| D | GLY146 |
| site_id | BC1 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE GTP L 501 |
| Chain | Residue |
| D | LEU248 |
| D | LYS254 |
| L | GLN11 |
| L | ALA12 |
| L | GLN15 |
| L | ALA99 |
| L | ASN101 |
| L | SER140 |
| L | GLY143 |
| L | GLY144 |
| L | THR145 |
| L | GLY146 |
| L | ILE171 |
| L | THR179 |
| L | GLU183 |
| L | ASN206 |
| L | TYR224 |
| L | ASN228 |
| L | MG502 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG L 502 |
| Chain | Residue |
| L | GLU71 |
| L | GTP501 |
| site_id | BC3 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE GDP I 501 |
| Chain | Residue |
| I | GLN11 |
| I | CYS12 |
| I | GLN15 |
| I | SER140 |
| I | GLY143 |
| I | GLY144 |
| I | THR145 |
| I | GLY146 |
| I | ASP179 |
| I | ASN206 |
| I | TYR224 |
| I | ASN228 |
| site_id | BC4 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE GTP A 501 |
| Chain | Residue |
| A | GLN11 |
| A | ALA12 |
| A | GLN15 |
| A | ASP98 |
| A | ALA99 |
| A | ALA100 |
| A | ASN101 |
| A | SER140 |
| A | GLY143 |
| A | GLY144 |
| A | THR145 |
| A | GLY146 |
| A | ILE171 |
| A | THR179 |
| A | GLU183 |
| A | ASN206 |
| A | TYR224 |
| A | ASN228 |
| A | MG502 |
| H | LEU248 |
| H | LYS254 |
| site_id | BC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG A 502 |
| Chain | Residue |
| A | GLU71 |
| A | GTP501 |
| site_id | BC6 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE GDP B 501 |
| Chain | Residue |
| B | GLN11 |
| B | CYS12 |
| B | GLN15 |
| B | SER140 |
| B | GLY143 |
| B | GLY144 |
| B | THR145 |
| B | GLY146 |
| B | ASP179 |
| B | ASN206 |
| B | TYR224 |
| B | ASN228 |
| site_id | BC7 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE GTP K 501 |
| Chain | Residue |
| B | LEU248 |
| B | LYS254 |
| K | GLN11 |
| K | ALA12 |
| K | GLN15 |
| K | ASP98 |
| K | ALA99 |
| K | ALA100 |
| K | ASN101 |
| K | SER140 |
| K | GLY143 |
| K | GLY144 |
| K | THR145 |
| K | GLY146 |
| K | ILE171 |
| K | THR179 |
| K | GLU183 |
| K | ASN206 |
| K | TYR224 |
| K | ASN228 |
| K | MG502 |
| site_id | BC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG K 502 |
| Chain | Residue |
| K | GLU71 |
| K | GTP501 |
| site_id | BC9 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE GDP H 501 |
| Chain | Residue |
| H | GLN11 |
| H | CYS12 |
| H | GLN15 |
| H | SER140 |
| H | GLY143 |
| H | GLY144 |
| H | THR145 |
| H | GLY146 |
| H | ASP179 |
| H | ASN206 |
| H | TYR224 |
| H | ASN228 |
Functional Information from PROSITE/UniProt
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| F | ASN228 | |
| G | GLN11 | |
| G | SER140 | |
| G | GLY144 | |
| G | THR145 | |
| G | GLY146 | |
| G | ASN206 | |
| G | ASN228 | |
| D | GLN11 | |
| D | SER140 | |
| D | GLY144 | |
| D | THR145 | |
| D | GLY146 | |
| D | ASN206 | |
| D | ASN228 | |
| I | GLN11 | |
| I | SER140 | |
| I | GLY144 | |
| I | THR145 | |
| I | GLY146 | |
| I | ASN206 | |
| I | ASN228 | |
| B | GLN11 | |
| B | SER140 | |
| B | GLY144 | |
| B | THR145 | |
| B | GLY146 | |
| B | ASN206 | |
| B | ASN228 | |
| H | GLN11 | |
| H | SER140 | |
| H | GLY144 | |
| H | THR145 | |
| H | GLY146 | |
| H | ASN206 | |
| H | ASN228 | |
| F | GLY144 | |
| F | THR145 | |
| F | GLY146 | |
| F | ASN206 | |
| N | SER162 | |
| M | SER162 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q6PER3 |
| Chain | Residue | Details |
| E | ASN206 | |
| E | ASN228 | |
| J | GLN11 | |
| J | GLU71 | |
| J | SER140 | |
| J | GLY144 | |
| J | THR145 | |
| J | THR179 | |
| J | ASN206 | |
| J | ASN228 | |
| C | GLN11 | |
| C | GLU71 | |
| C | SER140 | |
| C | GLY144 | |
| C | THR145 | |
| C | THR179 | |
| C | ASN206 | |
| C | ASN228 | |
| L | GLN11 | |
| L | GLU71 | |
| L | SER140 | |
| L | GLY144 | |
| L | THR145 | |
| L | THR179 | |
| L | ASN206 | |
| L | ASN228 | |
| A | GLN11 | |
| A | GLU71 | |
| A | SER140 | |
| A | GLY144 | |
| A | THR145 | |
| A | THR179 | |
| A | ASN206 | |
| A | ASN228 | |
| K | GLN11 | |
| K | GLU71 | |
| K | SER140 | |
| K | GLY144 | |
| K | THR145 | |
| K | THR179 | |
| K | ASN206 | |
| K | ASN228 | |
| N | SER176 | |
| M | SER176 | |
| D | GLU71 | |
| I | GLU71 | |
| B | GLU71 | |
| H | GLU71 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P99024 |
| Chain | Residue | Details |
| G | SER40 | |
| D | SER40 | |
| I | SER40 | |
| B | SER40 | |
| H | SER40 | |
| F | SER40 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P99024 |
| Chain | Residue | Details |
| G | LYS60 | |
| D | LYS60 | |
| I | LYS60 | |
| B | LYS60 | |
| H | LYS60 | |
| F | LYS60 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphoserine; by CDK1 => ECO:0000250|UniProtKB:Q13885 |
| Chain | Residue | Details |
| D | SER174 | |
| I | SER174 | |
| B | SER174 | |
| H | SER174 | |
| L | SER48 | |
| L | SER232 | |
| A | SER48 | |
| A | SER232 | |
| K | SER48 | |
| K | SER232 | |
| F | SER174 | |
| G | SER174 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 12 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P07437 |
| Chain | Residue | Details |
| I | THR287 | |
| I | THR292 | |
| B | THR287 | |
| B | THR292 | |
| H | THR287 | |
| H | THR292 | |
| F | THR292 | |
| G | THR287 | |
| G | THR292 | |
| D | THR287 | |
| D | THR292 | |
| F | THR287 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 6 |
| Details | MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:P07437 |
| Chain | Residue | Details |
| G | ARG320 | |
| D | ARG320 | |
| I | ARG320 | |
| B | ARG320 | |
| H | ARG320 | |
| F | ARG320 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | MOD_RES: 5-glutamyl polyglutamate => ECO:0000250|UniProtKB:Q2T9S0 |
| Chain | Residue | Details |
| G | GLU448 | |
| D | GLU448 | |
| I | GLU448 | |
| B | GLU448 | |
| H | GLU448 | |
| F | GLU448 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P07437 |
| Chain | Residue | Details |
| D | LYS60 | |
| B | LYS60 | |
| H | LYS60 | |
| G | LYS60 | |
| I | LYS60 | |
| F | LYS60 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 12 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P07437 |
| Chain | Residue | Details |
| I | LYS326 | |
| B | LYS326 | |
| H | LYS326 | |
| C | GLU445 | |
| G | LYS326 | |
| A | GLU445 | |
| D | LYS326 | |
| E | GLU445 | |
| F | LYS326 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 6 |
| Details | MOD_RES: 3'-nitrotyrosine => ECO:0000250|UniProtKB:Q71U36 |
| Chain | Residue | Details |
| J | TYR451 | |
| A | TYR451 | |
| C | TYR451 | |
| L | TYR451 | |
| K | TYR451 | |
| E | TYR451 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 18 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P68363 |
| Chain | Residue | Details |
| E | LYS326 | |
| E | LYS370 | |
| J | LYS326 | |
| J | LYS370 | |
| C | LYS326 | |
| C | LYS370 | |
| L | LYS326 | |
| L | LYS370 | |
| A | LYS326 | |
| A | LYS370 | |
| K | LYS326 | |
| K | LYS370 |
